Origin IGS: atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatttgcacatttcaaacaatatatatacccttgcggaaacaacagaaaaaggagttccgaaaagcaaggtctcaaagttaaacaatggattataaagat Mask Tandem Repeat Region ================================================ atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Find is-nt database================================================ Query_seq: PI0723:PI0724|PI0723:PI0724:conserved hypothetical protein:DNA polymerase III, delta subunit:->->:657440..657542 103 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0723:PI0724|PI0723:PI0724:conserved hypothetical protein:DNA polymerase III, delta subunit:->->:657440..657542 103 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0723:PI0724|PI0723:PI0724:conserved hypothetical protein:DNA polymerase III, delta subunit:->->:657440..657542 103 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M F I I H C L T L R P C F S E L L F L L F P Q G Y I Y C L K C A N I . Protein_Len: 30 Strand: - Start: 8 End: 97 ....... L G N N L K S V K S K P V G K E T T E A L T Y I N N S I H M ...... Protein_Len: 33 Strand: - Start: 3 End: 101 .. K I I W Q K V K L G Q K E S S R K R N N G C P Y I Y Q K F H A F M .. atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0723:PI0724|PI0723:PI0724:conserved hypothetical protein:DNA polymerase III, delta subunit:->->:657440..657542 103 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: pint_PI0723_PI0724|conserved hypothetical protein:DNA polymerase III, delta subunit|POSITIVE:POSITIVE|[657440,657542]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta atctttataatccattgtttaactttgagaccttgcttttcggaactcctttttctgttgtttccgcaagggtatatatattgtttgaaatgtgcaaatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUAUAAUCCAUUGUUUAACUUUGAGACCUUGCUUUUCGGAACUCCUUUUUCUGUUGUUUCCGCAAGGGUAUAUAUAUUGUUUGAAAUGUGCAAAUAUUA ..............................((((((.....(((((..(.......)..))))).))))))..........((((((.......))))))... (-13.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUUUGCACAUUUCAAACAAUAUAUAUACCCUUGCGGAAACAACAGAAAAAGGAGUUCCGAAAAGCAAGGUCUCAAAGUUAAACAAUGGAUUAUAAAGAU ................................(((((((....)..........((....)).....)))))).............................. (-11.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 67 24 128 79 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 319 67 23 95 50 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 299 65 23 65 14 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 298 76 32 222 182 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 287 77 31 51 2 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 286 67 31 184 147 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 282 79 31 134 70 pint:PI1742|5end_SpoOJ_regulator_protein_1664826..1665056_POSITIVE 275 72 32 86 49 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 270 74 33 171 122 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 270 74 33 64 15 pint:PI1984|5end_MutT/nudix_family_protein_1940184..1940414_POSITIVE 269 77 31 207 164 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 263 67 23 118 59 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 262 95 55 151 109 pint:PI0161|5end_possible_TonB_receptor_153364..153594_POSITIVE 261 73 32 103 62 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 259 70 21 50 8 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 258 60 12 231 184 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 258 66 26 228 185 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 257 57 12 72 25 pint:PI1554|5end_hypothetical_protein_1470275..1470505_POSITIVE 256 54 15 56 19 pint:PI0095|5end_hypothetical_protein_91444..91674_POSITIVE 255 97 51 184 132 pint:PI1385|5end_3-deoxy-d-manno-octulosonic_acid_8-phosphate_synthase_(DAHP_synthase,_Class_I)_1306224..1306454_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 68 30 133 94 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 275 73 32 110 66 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 275 72 32 102 65 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 274 74 32 150 112 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 263 67 23 122 63 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 261 73 32 83 42 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 258 60 12 116 69 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 256 54 15 69 32 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 255 97 51 54 2 pint:PI1384|3end_conserved_hypothetical_protein_1306174..1306324_POSITIVE 255 73 34 144 93 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 253 69 22 65 15 pint:PI1629|3end_hypothetical_protein_1551966..1552116_POSITIVE 250 64 22 97 56 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 248 68 24 151 107 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 246 70 24 149 97 pint:PI0987|3end_hypothetical_protein_912284..912434_POSITIVE 246 36 2 139 104 pint:PI0009|3end_NAD-dependent_epimerase/dehydratase_family_protein_10674..10824_POSITIVE 245 74 33 126 88 pint:PI1700|3end_hypothetical_protein_1619243..1619393_POSITIVE 244 86 41 69 26 pint:PI1828|3end_peptidase,_M23/M37_family,_C-terminal_1769089..1769239_POSITIVE 243 76 32 60 20 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 239 74 32 103 58 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 238 86 41 84 26 pint:PI0577|3end_conserved_hypothetical_protein_522700..522850_POSITIVE